College of Agriculture and Life Sciences Honors Theseshttp://hdl.handle.net/1813/29372015-08-02T20:33:21Z2015-08-02T20:33:21ZThe Effect of Temperature Change on Viral Pathogenesis of Viral Hemorrhagic Septicemia Virus (VHSV) in Fathead Minnow (Pimephales promelas)Fellman, Rebeccahttp://hdl.handle.net/1813/405312015-07-24T05:00:59Z2012-05-01T00:00:00ZThe Effect of Temperature Change on Viral Pathogenesis of Viral Hemorrhagic Septicemia Virus (VHSV) in Fathead Minnow (Pimephales promelas)
Fellman, Rebecca
Viral hemorrhagic septicemia virus (VHSV) prevalence in Great Lakes fish populations varies seasonally, with greater prevalence during spawning seasons. Chronic infections appear to be associated with neural tissue, while acute forms target endothelial tissue. Given the potential immunosurpessive effect of water temperature variation in natural environments, I investigated the effect of a 5ºC temperature change on disease development due to VHSV infection in fathead minnow Pimephales promelas. Fish were exposed to VHSV genotype IVb and either a temperature increase from 10ºC to 15ºC, decrease from 20ºC to 15ºC, or a stable temperature of 15ºC. I evaluated prevalence of gross lesions and death, tested fish for VHSV via cell culture of pooled visceral tissue, and performed quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays on brain tissue and pooled visceral tissue extracts. Fish that experienced temperature decrease had greater VHSV prevalence than those that experienced temperature increase, and more tested positive by qRTPCR of brain tissue than those that experienced no change, suggesting greater prevalence of infections. Visceral organ samples from fish that experienced either temperature change contained higher viral RNA N-gene copy numbers than those from fish that experienced stable temperature, while brain tissue
samples contained similar viral RNA copy numbers among all groups. In fish that contained more viral RNA copies in viscera than brain, those fish that experienced either temperature change had a greater difference between the two quantities than those that experienced no temperature change. The severity of chronic infections was not affected by temperature change, but the severity of acute infections was increased in fish that experienced any temperature change. These results suggest that fish that encounter temperature changes, especially decreases, of 5ºC are at higher risk of contracting chronic VHSV infections and severe acute VHSV infections, helping to explain seasonal fish die-offs attributed to VHSV, especially in fish that encounter temperature change during the spawning season.
2012-05-01T00:00:00ZHCF-1 inhibits SKN-1 to Modulate Stress Resistance but Not lifespan in Caenorhabditis Elegans AND Determination of Enrichment Regions for H3K27me3 and Other low-signal, High-noise ChIP-seq DataPicard, Colette L.http://hdl.handle.net/1813/404872015-07-18T05:05:53Z2012-05-01T00:00:00ZHCF-1 inhibits SKN-1 to Modulate Stress Resistance but Not lifespan in Caenorhabditis Elegans AND Determination of Enrichment Regions for H3K27me3 and Other low-signal, High-noise ChIP-seq Data
Picard, Colette L.
1) Caenorhabditis elegans host cell factor-1 (HCF-1) is an evolutionarily conserved longevity determinant. HCF-1 modulates both lifespan and stress resistance by inhibiting the C. elegans homolog of the mammalian FOXO transcription factors, DAF-16. However, the involvement of other components in HCF-1 mediated longevity and stress resistance has not yet been characterized. We show that SKN-1, the C. elegans homolog of the mammalian Nrf proteins and a major orchestrator of the phase II detoxification response that defends against oxidative stress, is regulated by HCF-1 to modulate oxidative stress resistance but not lifespan. Our findings imply a novel regulatory relationship between HCF-1 and SKN-1 that is revealed only in the presence of oxidative stress.
2) Chromatin modifications are a major mechanism through which cells regulate gene expression. ChIP-seq allows for genome-wide profiling of any DNA-binding protein, including histones. To analyze these data, researchers have developed statistical tools that can identify genomic regions enriched for the DNA-binding protein of interest. Some histone marks, however, bind across broad regions of the genome and produce diffuse and high-noise data profiles that are often difficult to analyze. In this paper, I investigate the ability of peak-callers to analyze ChIP-seq data from H3K27me3, a histone mark known to produce broad regions of enrichment. Further, I present an alternative method that is both faster and simpler than the than the other peak callers investigated. This alternative method offers promise in identifying enriched genomic features when a histone mark, like H3K27me3, generates very diffuse and noisy ChIP-seq data patterns.
2012-05-01T00:00:00ZExpression of Downstream Targets of mTOR in Response to a Model of Maternal Undernutrition and HypoxiaGroth, Jessica L.http://hdl.handle.net/1813/404862015-07-18T05:05:51Z2012-05-01T00:00:00ZExpression of Downstream Targets of mTOR in Response to a Model of Maternal Undernutrition and Hypoxia
Groth, Jessica L.
The mammalian target of rapamycin (mTOR) is a key player in a signaling pathway that regulates cell growth in response to nutrients, hypoxia, and other upstream regulators. To examine the effects of nutrient restriction, hypoxia, and their possible interactive effects on placental mTOR, a series of experiments were carried out on immortalized human placental trophoblasts. To assess the temporal response, trophoblasts grown in nutrient replete (complete; C) and nutrient restricted (NR) media were harvested at 0 to 96h; phosphorylated s6 ribosomal protein (s6rp) and eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) protein levels were measured using western analysis. To assess the independent and interactive effects of NR and hypoxia (Hx) on mTOR, trophoblasts were grown in C and normoxia (20% oxygen;Nx), C media and Hx (1% oxygen), NR -Nx, NR -Hx and harvested at72h; total and phosphorylated s6rp protein levels were measured using western analysis. NR had a negative temporal effect on
phosphorylation of s6rp and 4E-BP1. Maximal change occurred at 48h for p-s6rp and at 72h for p-4E-BP1. NR alone had no effect on total protein expression of s6rp under Nx or Hx, whereas Hx decreased total protein expression of s6rp in C media samples at 72h. NR alone decreased ps6rp but Hx alone had no effect on p-s6rp at 72h. NR and Hx interacted to affect p-s6rp such that Hx reduced p-s6rp in C media but slightly increased it in NR media. The interactive effect of Hx and NR suggest that the mechanisms by which nutrients and Hx affect mTOR signaling have not been fully elucidated, and may shed light on how these two conditions contribute to placental complications such as intrauterine growth restriction and preeclampsia.
2012-05-01T00:00:00ZPutting a Dent in Our Understanding of Maize Kernel MorphologyMurray, Matthew D.http://hdl.handle.net/1813/373182015-07-08T20:29:59Z2014-08-29T00:00:00ZPutting a Dent in Our Understanding of Maize Kernel Morphology
Murray, Matthew D.
Much of our modern maize germplasm was originally brought about by the combination of northern flint lines and southern dent lines. Yet commercial production in the US today is dominated by dent or semi-dent kernel type maize (Corn Belt dent), which has hard outer walls of endosperm surrounding a soft floury interior that when dried compacts to form the characteristic dent in the top of the kernel. One major exception is flint type corn, which is grown in areas of North America, Europe, South America, the Caribbean and many parts of Africa. Flint maize is characterized by its rounded vitreous outer endosperm and soft granular center and has desirable qualities such as cold tolerance, disease and insect resistance as well as longer storage capacity than many dent lines.
The Nested Association Mapping (NAM) population parent inbred lines represent many of the major kernel types found in maize. In 2006 the entire NAM population of recombinant inbred lines were grown and scored visually for kernel type, in five locations. The NAM population contains 25 parents, of which, there are nine flint, nine semi-dent, four dent, two sweet and one popcorn parent lines, with a common dent parent, B73. Linkage mapping with ~7400 intervals markers was used to examine the genetics of kernel morphology. This yielded several areas of the genome that are significantly associated with the difference in kernel type seen in NAM. Several other major and minor QTL are shared across many families. Genome wide association study (GWAS) was also used in the maize association panel. Suggested peaks from both linkage mapping and GWAS highlight 13 candidate genes in starch and protein related pathways in the endosperm.
2014-08-29T00:00:00ZIdentifying Genes that Interact with Calcineurin During Egg Activation in Drosophila melanogasterZuckerman, Rebecca M.http://hdl.handle.net/1813/373172015-07-08T20:29:41Z2014-08-29T00:00:00ZIdentifying Genes that Interact with Calcineurin During Egg Activation in Drosophila melanogaster
Zuckerman, Rebecca M.
When an egg is fertilized, before the new embryo can begin to develop, the egg must be “activated.” The process of activation triggers the egg to complete meiosis, to begin translating new proteins, to degrade proteins and RNAs that are no longer required, and to modify its membranes to form a harder outer covering. The universal signaling event is an increase in calcium levels that occurs in the egg at this time. In many cell types, calcium causes changes through a conserved signaling pathway by binding to a protein called calmodulin, which in turn regulates the activities of other proteins.
Calcineurin, a phosphatase, is one of those other proteins. It has been proven experimentally that calcineurin plays a critical role in regulating egg activation in fruit flies and in frogs. For example, Drosophila females expressing a constitutively active calcineurin (cnA-act) in their germline are sterile. To identify the proteins in the pathway by which calcineurin regulates egg activation, the Toshiro Aigaki lab tested whether there were Drosophila genes that interact genetically with calcineurin mutations. To do this, they searched for chromosomal regions whose deletion suppresses the sterility of cnA-act female flies. Fourteen large chromosomal regions were identified.
To define the precise gene(s) within each region that suppresses the sterility of cnA-act females, I have tested smaller deletions, and then individual mutations, within the five regions I am examining for interaction with cnA-act. For three of the deletions, I have identified a gene or genes whose mutants significantly restore fertility of cnA-act females, and thus is a candidate to act within the calcineurin pathway. The first is CG6927, a gene that is expressed in the ovary but currently has no known function. The second is eIF3-S8, a transcription initiation factor. The third is RpS24, a ribosomal protein. The fourth is CG42565, which like CG6927, has no known function. In the other two regions, I have narrowed down the cnA-act interacting genes to a small number of candidates, instead of the hundreds of genes within the original large region. I am currently testing the remaining candidates.
2014-08-29T00:00:00ZIsolation of Bacteria from Compost for Potential Use in BiodecaffeinationDivine, Roberthttp://hdl.handle.net/1813/373162015-07-08T13:20:24Z2014-08-29T00:00:00ZIsolation of Bacteria from Compost for Potential Use in Biodecaffeination
Divine, Robert
Caffeine (1,3,7-trimethyl xanthine) is a bioactive compound present in common foods and beverages such as coffee, tea, and chocolate. Though many consumers value caffeine for its physiological effects, others may prefer decaffeinated products to avoid caffeine. Decaffeination technologies have a great economic and environmental impact; however, current methods have various disadvantages, such as cost, waste, and solvent use. Microbial methods, known as biodecaffeination, have been explored as alternatives. Various microbes that are able to metabolize caffeine have been isolated from coffee plant roots. To this point, compost has not been looked at as a potential source for decaffeinating microbes.
Our objective was to isolate and identify microorganisms from compost and to address their potential as biodecaffeinators. Compost samples were obtained and then grown in nutrient broth. Cultures were streaked onto a selective agar that contained caffeine as its only carbon source. Partial 16S rDNA sequences were obtained for a subset of the colonies isolated from the caffeine agar. Preliminary results suggested that the isolated strains were Pseudomonas, Arthrobacter, Sphingobacterium, Streptomyces, and Paenibacillus, and that they may be capable of metabolizing caffeine.
2014-08-29T00:00:00ZAn Investigation of Microclimatological Conditions Along Elevation Transects Near Ithaca, NYRaymond, Colin S.http://hdl.handle.net/1813/373152015-07-08T12:28:40Z2014-08-29T00:00:00ZAn Investigation of Microclimatological Conditions Along Elevation Transects Near Ithaca, NY
Raymond, Colin S.
A field campaign was conducted in complex topography near Ithaca, NY with the aim of determining and describing both qualitatively and quantitatively the variables that affect nighttime temperatures there. Observations were compared against a weighted average of nearby private-weather-station readings and Rapid Refresh [RAP]-model gridpoint forecasts for the corresponding time periods. Local nowcasts or forecasts for locations along the transects — generated from a similarity analysis of station and transect-location metadata — showed generally poor skill, though the consistently greater errors at higher elevations suggest the potential for fruitful additional adjustments beyond the scope of this study. A distinct reversal in the upslope wind corresponding to lapse rates near the moist-adiabatic value supports the hypothesis of a triggered hilltop cold-air pool. Nights with strong potential-temperature inversions had remarkably similar synoptic-scale conditions, which bore the hallmarks of a valley inversion being entrained from above by warm southeast winds. Bolstering this hypothesis was the definite linear relationship found between observed lapse rates and region-wide temperature trends on clear nights, but not cloudy ones. To better account for these findings, a new forecast scheme was then implemented, combining regressions of observed along-transect lapse rates on upslope winds, modeled open-sky lapse rates, and region-wide temperature trends; it demonstrated improved skill over the station-based one, suggesting that further work to enable standardization of microclimatic forecasts based on a simple set of externally measured variables would be both possible and productive.
2014-08-29T00:00:00ZIdentification of Major Histocompatibility Complex Haplotypes in Icelandic HorsesViolette, Nathaniel P.http://hdl.handle.net/1813/373142015-07-08T12:23:06Z2014-08-29T00:00:00ZIdentification of Major Histocompatibility Complex Haplotypes in Icelandic Horses
Violette, Nathaniel P.
The Major Histocompatibility Complex (MHC) is a region of the vertebrate genome that encodes many immune-related proteins. The most well-known proteins that are encoded in this region are the MHC class I and MHC class II cell surface proteins. These proteins are integral in producing the adaptive immune response. Using polymorphic microsatellites within the MHC, MHC haplotypes were characterized from an extended Icelandic horse family of half and full siblings. The herd is composed of one stallion, fifteen dams, and three sets of foals from each dam. A total of nine microsatellite loci were tested: two in the MHC class I region, two in the MHC class III region, and five in the MHC class II region. The Icelandic herd displayed a large degree of diversity in this region even though the population has been isolated and affected by bottleneck events in the past. From the 32 possible unique haplotypes belonging to the one founder stallion and 15 mares, 26 unique haplotypes were identified. A MHC recombination event occurred on one of the paternal chromosomes. The stallion also exhibited segregation distortion in the distribution of the stallion’s MHC haplotypes inherited by the foals but not the sex ratio of the offspring. These findings suggest that the Icelandic horse population has a greater degree of diversity in the MHC region than most other commonly studied horse breeds. This diversity may come from a recombination mechanism that produces unique haplotypes by crossing over of existing haplotypes in the population at a higher rate than found in larger populations. Another possible explanation would be that less favorable MHC haplotypes are allowed to persist in the less immunologically selective environment of Iceland.
2014-08-29T00:00:00ZEffects of Photoperiod on Novelty Preference in Preadolescent Siberian Hamster (Phodopus sungorus) PupsBarrett, Colleen A.http://hdl.handle.net/1813/373132015-07-08T12:23:00Z2014-08-29T00:00:00ZEffects of Photoperiod on Novelty Preference in Preadolescent Siberian Hamster (Phodopus sungorus) Pups
Barrett, Colleen A.
Photoperiod (day length) has been shown to have significant effects on the physical and behavioral development of seasonally breeding mammals and to modulate the timing of their dispersal from the natal burrow or den. Behaviors associated with dispersal, such as novelty preference and exploratory behaviors, have been shown to be modulated by anti-Müllerian hormone (AMH) in mice. Whereas photoperiodic modulation of serum AMH concentrations in female Siberian hamsters (Phodopus sungorus) has been demonstrated, novelty preference and exploratory behaviors have not been previously investigated in this species. Through the manipulation of day length (DL) in Siberian hamsters, this study sought to determine if photoperiod-induced differences in serum AMH concentration correlate with behaviors that are associated with dispersal. Although AMH was significantly different in males and females, and day length had a significant effect on AMH in males, our evaluations of novelty preference and exploratory behaviors revealed no effects of sex or photoperiod when evaluated at 21 days of age. The information acquired from this study will contribute to the understanding and characterization of the associations among DL, AMH, and the behaviors associated with the dispersal of adolescent mammals. Utilizing this study’s results, future research is required to determine the age at which sex differences in novelty preference and exploratory behavior are first apparent in Siberian hamsters and to evaluate variations in AMH associated with age, sex, and photoperiod.
2014-08-29T00:00:00ZStart to Finish Detection of Cryptosporidium for in Field Use on Water Samples via Lauroylsarcosine sodium Salt (LSS) Extraction, Loop Mediated Isothermal Amplification (LAMP), and DNA PrecipitationWessling, Emilyhttp://hdl.handle.net/1813/373122015-07-08T12:18:38Z2014-08-29T00:00:00ZStart to Finish Detection of Cryptosporidium for in Field Use on Water Samples via Lauroylsarcosine sodium Salt (LSS) Extraction, Loop Mediated Isothermal Amplification (LAMP), and DNA Precipitation
Wessling, Emily
Today, many diseases that are rare in developed nations are still prevalent in other countries due to limited technological access and resources. Among these diseases is Cryptosporidiosis, a common gastro-intestinal infection with currently no known treatments. Cryptosporidiosis is caused by the parasite Cryptosporidium. This parasite spreads through the environment as an oocyst, causing self-limiting diarrhea in healthy humans. These symptoms are often more dangerous in immuno-compromised individuals and children, whose immune systems are still developing. The rugged Cryptosporidium oocysts are able to survive treatment with most disinfectants. Thus, to prevent outbreaks, there must be early detection, followed by rapid treatment of the water supply and/or limited exposure to infected water supplies. Current methods of parasite testing for water samples are limited in their function by cost, access to materials, and ability to run equipment. Improvements in cost-effective, easy to use alternatives to traditional techniques, such as the use of lauroylsarcosine sodium salt (LSS) for DNA extraction and the loop mediated isothermal amplification (LAMP) method of amplification, will facilitate the detection of Cryptosporidium in the field and in impoverish nations.In this experiment, a five primer LAMP reaction was used in combination with the LSS reaction to eliminate otherwise essential electrical equipment in the detection process, expediting and easing in-field detection. The LSS was found to decrease the efficiency of the LAMP reaction, but its effects were mediated by changing the buffer used in the LAMP reaction. Amplicons were visualized using gel electrophoresis in this experiment. However, methods of detection were tested for incorporation into the test. These techniques will lead to the future of cost efficient detection of Cryptosporidium in water samples.
2014-08-29T00:00:00Z